1. Research Discovery, Social Networks and
VIVO
Chicago, October 8, 2012
Michael Conlon, PhD
Clinical and Translational Science Institute
University of Florida
5. Research Process 2012
Create
Augment
Virtual
Hypothesis Data
Organi-
Systems
zation
Conduct
Get
Consults Experi-
Funded
ments
Assemble Write Publish Archive
Team proposal results data
11. 5. Competition rises
2011 Shanghai ranking of world universities
http://en.wikipedia.org/wiki/Academic_Ranking_of_World_Universities
Lots of Competitors
21. Software reads VIVO
RDF and displays
processOrg<-function(uri){
x<-xmlParse(uri)
u<-NULL
name<-xmlValue(getNodeSet(x,"//rdfs:label")[[1]])
subs<-getNodeSet(x,"//j.1:hasSubOrganization")
if(length(subs)==0) list(name=name,subs=NULL)
else {
for(i in 1:length(subs)){
sub.uri<-
getURI(xmlAttrs(subs[[i]])["resource"])
u<-c(u,processOrg(sub.uri))
}
list(name=name,subs=u)
}
}
VIVO produces both
HTML and RDF
22. Co-Author Network
Chris McCarty, Assoc. Prof. & Raffaele Vacca
200 201
8 2
• Data source: Thomson Reuters via UF VIVO
• Each node represents one author
• Nodes are sized by Total Publications and linked by a common VIVO publication URI
Main Component: what changes have occurred between 2008 and 2012?
• In 2008 the network is split into two groups of approximately the same size – CTSI/HSC versus everything else
• In 2012 the network consists of one big connected region, with the CTSI acting as a broker between several more
marginal subgroups
• In 2012 more of the authors with the highest number of publications are under the CTSI umbrella (note that 2012
publications data are incomplete)
23. Co-Funded Network
Chris McCarty, Assoc. Prof. & Raffaele Vacca
200 201
8 2
• Data source: UF Division of Sponsored Research (DSR) database
• Each node represents one Contract PI, Project PI or Co-PI linked by a common PeopleSoft Contract number
• Nodes are sized by Total Awarded in UF fiscal year (July-June)
Main Component: what changes have occurred between 2008 and 2012?
• More of Health Science Center comes under the CTSI umbrella
• The CTSI has a broader reach in the whole network
• Increasingly the CTSI incorporates all researchers in relevant areas (areas not relevant to CTSI
research fields naturally remain out of its network)
29. 4th Annual VIVO Conference
August 14-15, 2013
St. Louis, Missouri, USA
http://vivoweb.org/conference
Editor's Notes
Learned a field, learned the scientific methods, did science, wrote papers
Science and scientists. Biochemistry at Stanford. They look happy.
The rise of molecular medicine
The rise of the molecular. Personalized medicine. Full base pair sequencing. Mars Curiosity lander. Nanotechnoloy. Metabolomics.
Rapid increase in volume of scientific output. Brazil, Russia, India, China.
More difficult problems. We work to cure cancer. Risk factors, genetics, metabolics, surgical procedures, radiology, chemotherapy, life style changes.
Data got big. Terabytes, Petabytes, Exabytes.
Competition got stiffer
Internet speed and disintermediation. Expectations changing, openness, commonality, reuse, altmetrics (“downloads and citations”)
Research Discovery. What is going on? Where? By Whom?
Sounds, common data models for the things of science and the connections between them. Many kinds of connections between each type of object. Objects have significant complexity. What do we mean by “project” – a human subject study? A clinical trial?
So that’s what we are doing. Open software, community and data model for research discovery. Model people, data, projects, papers, etc. Work across boundaries. Sponsor supported.
So here’s the simple view – a faculty profile. Assembled by machines. Can be finished off by the faculty member. All links are to other objects in the semantic web. Positions, visualizations, organizations, people, web sites. Navigation via search, facets, link traversal. Note the RDF link for techno guys.
A fragment of the VIVO ontology. Open ontology process. Working group. Plug-in ontologies (BIBO, SKOS, FOAF) support local extension. Terminology extensions.
Tools for discovering research. Here, sample of University of Florida publications plotted on the UCSD science.
The open architecture of VIVO and linked data supports development of applications outside VIVO that consume VIVO data. VIVO data is accessible via HTML (for humans) and RDF (for machines). Simple software can process the RDF resulting in powerful cross-site applications. The figure depicts the organization of the University of Florida.
Mention that 2012 data come from only half of the year. As a consequence: (1) Less nodes in 2012 network (less authors in 2012 data); (2) Node sizes smaller on average in 2012 (less publications in 2012 data)
Vivosearch (beta) indexes vivo sites and provides faceted search across the collection with linking to individual objects
VIVO searchlight. For any page on the web, find people whose work is similar to a page you are reading.
We are going to need a community of people who share a common interest in research discovery.